[English] 日本語
Yorodumi- PDB-5cch: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cch | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form) | ||||||
Components |
| ||||||
Keywords | ENDOCYTOSIS / EXOCYTOSIS / synaptic fusion complex / Synaptotagmin1 / neuronal SNARE complex | ||||||
Function / homology | Function and homology information trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / calcium ion sensor activity / regulation of regulated secretory pathway / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / zymogen granule membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / vesicle fusion / regulation of calcium ion-dependent exocytosis / vesicle docking / positive regulation of calcium ion-dependent exocytosis / exocytic vesicle / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / positive regulation of dendrite extension / Golgi to plasma membrane protein transport / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / protein localization to membrane / calcium-dependent phospholipid binding / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / myosin binding / regulation of dopamine secretion / exocytosis / phosphatidylserine binding / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / positive regulation of excitatory postsynaptic potential / protein sumoylation Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Zhou, Q. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Weis, W.I. / Brunger, A.T. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. ...Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. / Lemke, H.T. / Pfuetzner, R.A. / Choi, U.B. / Weis, W.I. / Diao, J. / Sudhof, T.C. / Brunger, A.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cch.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cch.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cch_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5cch_full_validation.pdf.gz | 475.2 KB | Display | |
Data in XML | 5cch_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 5cch_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/5cch ftp://data.pdbj.org/pub/pdb/validation_reports/cc/5cch | HTTPS FTP |
-Related structure data
Related structure data | 5ccgC 5cciC 5ccjC 1n7sS 1uowS 3f04S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
| ||||||||||||||||||
Details | Authors state that the biological assembly includes Chain A, B, C, D, Chain E 273-421, Chain F 273-421, Chain F 141-265 from symmetric neighbor. |
-Components
-Protein , 3 types, 4 molecules ABEF
#1: Protein | Mass: 7231.061 Da / Num. of mol.: 1 / Fragment: UNP residues 28-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63045 |
---|---|
#2: Protein | Mass: 7837.957 Da / Num. of mol.: 1 / Fragment: UNP residues 191-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851 |
#5: Protein | Mass: 32247.197 Da / Num. of mol.: 2 / Fragment: UNP residues 141-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707 |
-Synaptosomal-associated protein ... , 2 types, 2 molecules CD
#3: Protein | Mass: 9030.114 Da / Num. of mol.: 1 / Fragment: UNP residues 7-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881 |
---|---|
#4: Protein | Mass: 7471.368 Da / Num. of mol.: 1 / Fragment: UNP residues 141-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881 |
-Non-polymers , 1 types, 7 molecules
#6: Chemical | ChemComp-CA / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 27, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.6→50 Å / Num. obs: 20922 / % possible obs: 99.7 % / Redundancy: 14.5 % / Biso Wilson estimate: 133.06 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.105 / Χ2: 0.584 / Net I/av σ(I): 24.6 / Net I/σ(I): 4 / Num. measured all: 302949 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N7S,3F04,1UOW Resolution: 3.6→48.29 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.05 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 157.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→48.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|